chr6-156777698-A-AGCGGCGGCG
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP3BP6_ModerateBS1BS2
The NM_001374828.1(ARID1B):c.34_42dup(p.Ala12_Ala14dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.015 in 143,572 control chromosomes in the GnomAD database, including 24 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.015 ( 24 hom., cov: 31)
Exomes 𝑓: 0.0051 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
ARID1B
NM_001374828.1 inframe_insertion
NM_001374828.1 inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.09
Genes affected
ARID1B (HGNC:18040): (AT-rich interaction domain 1B) This locus encodes an AT-rich DNA interacting domain-containing protein. The encoded protein is a component of the SWI/SNF chromatin remodeling complex and may play a role in cell-cycle activation. The protein encoded by this locus is similar to AT-rich interactive domain-containing protein 1A. These two proteins function as alternative, mutually exclusive ARID-subunits of the SWI/SNF complex. The associated complexes play opposing roles. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP3
?
Nonframeshift variant in repetitive region in NM_001374828.1
BP6
?
Variant 6-156777698-A-AGCGGCGGCG is Benign according to our data. Variant chr6-156777698-A-AGCGGCGGCG is described in ClinVar as [Likely_benign]. Clinvar id is 1199905.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.015 (2158/143572) while in subpopulation NFE AF= 0.0222 (1444/65054). AF 95% confidence interval is 0.0212. There are 24 homozygotes in gnomad4. There are 961 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High AC in GnomAd at 2161 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARID1B | NM_001374828.1 | c.34_42dup | p.Ala12_Ala14dup | inframe_insertion | 1/20 | ENST00000636930.2 | |
LOC115308161 | NR_163974.1 | n.274-268_274-267insCGCCGCCGC | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARID1B | ENST00000636930.2 | c.34_42dup | p.Ala12_Ala14dup | inframe_insertion | 1/20 | 2 | NM_001374828.1 | A2 | |
ENST00000603191.2 | n.178-268_178-267insCGCCGCCGC | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0151 AC: 2161AN: 143520Hom.: 24 Cov.: 31
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00506 AC: 16AN: 3162Hom.: 0 Cov.: 0 AF XY: 0.00467 AC XY: 7AN XY: 1498
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Data not reliable, filtered out with message: AS_VQSR
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GnomAD4 genome ? AF: 0.0150 AC: 2158AN: 143572Hom.: 24 Cov.: 31 AF XY: 0.0138 AC XY: 961AN XY: 69810
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 24, 2019 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at